Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate WP_012760079.1 RLEG_RS33530 ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_000023185.1:WP_012760079.1
          Length = 510

 Score =  384 bits (986), Expect = e-111
 Identities = 207/496 (41%), Positives = 302/496 (60%), Gaps = 2/496 (0%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V+++I V+KRFGD +AN  +++ L KGE+ ALLGENGAGK+TLM+IL G   P  G + +
Sbjct: 5   VLEIIGVSKRFGDNLANHDISMTLAKGEVVALLGENGAGKTTLMSILFGHYMPDAGRILI 64

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
           +G       P  A   G+GMVHQHF L    TV EN++ G E           A+KK+L 
Sbjct: 65  EGTEVPQGKPRAAIRAGVGMVHQHFSLAPNLTVLENVMTGTERLWSWRSATSAARKKLLT 124

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
           +S R+GL V+PDA + D+SVG+QQRVEILK LY  A ILI DEPTAVLT  E   L   +
Sbjct: 125 ISGRFGLKVDPDARLGDLSVGEQQRVEILKALYNDARILILDEPTAVLTNIEAERLFTTL 184

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245
           + +  +G S+I I+HKLDE+ A ADRI V+R GK +   +  + +  ELAELMVGR V+ 
Sbjct: 185 REMAHQGLSLIFISHKLDEVMAAADRIVVLRGGKMVAERKASETSKAELAELMVGRRVTR 244

Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305
              + +  P  V LE   + ++   G  ++K +S  +  GEI+G+ G+ GNGQ  L   +
Sbjct: 245 PVREPST-PGAVALEASGVTVRID-GVDRLKSISFRLHQGEILGIIGVSGNGQAALAHLL 302

Query: 306 TGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYK 365
           +G     +G + L  + I N     + +  +G +PEDR+ +G++ EM + EN  L+    
Sbjct: 303 SGTLARSAGDLMLFGEAIGNLGVADVVDAGIGRIPEDRNEEGVIGEMAIWENAVLERLAS 362

Query: 366 PPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLL 425
           P  S++G ++     + A E+++ FDVRG G  +    LSGGN QK I+ R + R P +L
Sbjct: 363 PAFSRHGLVNRKAGMAFASEIIDGFDVRGGGPAIRTRLLSGGNMQKLILGRNLHRRPRIL 422

Query: 426 IVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIV 485
           I +QP RGLD GA+  +H RL++AR +G AVL+IS +LDE++ ++DRI  I  G++   V
Sbjct: 423 IAAQPARGLDEGAVAAVHARLLEARRQGTAVLLISEDLDEVIALADRIQAIVVGRLSPPV 482

Query: 486 SPETTTKQELGILMVG 501
             +    + LG++M G
Sbjct: 483 EADGADARRLGLMMAG 498



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 66/250 (26%), Positives = 111/250 (44%), Gaps = 15/250 (6%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           VLEI  ++ K    +L    +S+ +  GE+V + G +G G+T L+  + G    D+G I 
Sbjct: 5   VLEIIGVS-KRFGDNLANHDISMTLAKGEVVALLGENGAGKTTLMSILFGHYMPDAGRIL 63

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377
           +   ++   +PR      VG V +      L   +TV EN+   T             + 
Sbjct: 64  IEGTEVPQGKPRAAIRAGVGMVHQ---HFSLAPNLTVLENVMTGTER--------LWSWR 112

Query: 378 KINSHARELMEEFDVR---GAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGL 434
              S AR+ +     R             LS G QQ+  I + +  +  +LI+ +PT  L
Sbjct: 113 SATSAARKKLLTISGRFGLKVDPDARLGDLSVGEQQRVEILKALYNDARILILDEPTAVL 172

Query: 435 DVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQE 494
                E +   L +   +G +++ IS +LDE++  +DRI V+  G++        T+K E
Sbjct: 173 TNIEAERLFTTLREMAHQGLSLIFISHKLDEVMAAADRIVVLRGGKMVAERKASETSKAE 232

Query: 495 LGILMVGGNI 504
           L  LMVG  +
Sbjct: 233 LAELMVGRRV 242


Lambda     K      H
   0.315    0.135    0.365 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 662
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 506
Length of database: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources